For more than 3 variants, rate update is incorrect

[sangeetabhatia03]

From Pierre,
rate <- lambda[t, , 1] +
apply(epsilon * lambda[t, , -1, drop = FALSE], c(1, 2), sum) + # something fishy here with the sum given epsilon can be >1Dim
1 / priors$R$scale

[11:32] Nouvellet, Pierre

I think this bit is problematic: apply(epsilon * lambda[t, , -1, drop = FALSE], c(1, 2), sum) as, say for 2 variants, we want to multiply each epsilon to lambda[t,,2] and then lambda[t,,3]

Pierre suggests that a quick fix would be to replace the line mentioned above by:
temp <- lambda[t, , 1]
for(i in 2:dim(incid)[3]){
temp <- temp + epsilon[i-1]*lambda[t, , i]
}
rate <- temp + 1 / priors$R$scale

[sangeetabhatia03]

I have implemented Pierre's suggestion and all tests pass OK. But I am not sure I fully understand. I think the previous implementation was achieving the right updates (epsilon_v * lambda^t_v for each t).
Branch fix_122, commit 72d26f6